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Just posting this in case some one searches and finds this thread. Info about swapping the transmission.

-- Mating Engine & Transmission --

The best method is outside car, which means pulling out the entire drivetrain.

This was a big gotcha for me. Once you unbolt the two they come apart relatively easy. Putting them back together is the same way. The dowels will align them and they should slide together flush. DO NOT USE THE BOLTS TO BRING THEM TOGETHER. If they are not coming together correctly its not the dowels, its the alignment of the torque convertor or the clutch. I did not realize this and on the 3rd time of using the bolts to draw them together we heard a large bang which sounded it came from inside the transmission. Because I didn't want to chance having to do all this work again I went ahead and bought another transmission ($850 used).

We then came up with a much better process. Put both the engine and transmission upright on the ground. Turn the engine crankshaft until one of the holes on the flywheel lines up with the cutout for the starter(remember only turn the engine clockwise when looking at it from the crankshaft pulley side, if you miss a bolt, just keep turning until it comes around again). Put the torque converter inside the transmission and try putting it on the shaft. Very important to note the cutouts at the back of the shaft that match the shape of the tabs on the torque converter. You should be able to push the torque convertor all the way back to the point that you can't stick your finger behind the torque converter. Once the converters in place, rotate it until one of the 4 studs lines up with the hole in the flywheel you can see through the starter cutout. Then slowly bring the engine and transmission together. Let the 2 dowels line them up, and make sure the torque converter slides through the hole. Then the engine and trans should be able to be pushed flush against each other by hand. At this point the torque converter will probably be a little too far back to get a nut on the stud. You can reach in with your finger and pull it forward against the flywheel. Then start putting nuts on. I used some locktite as I put them on. You need to put the nuts nearly all the way on the thread, don't make them tight just yet, but if you don't put the nut all the way down they will rub against the engine block as you rotate the flywheel to get to the next studs.

Since I replaced the transmission the service manual says several times not to drive the car until its been hooked up to Nissans CONSULT III diagnostic system so that some memory can be cleared. The car has about 150 miles on it so far and the transmission behaves fine and theres no warning light or anything present, so I don't think that part is necassary.
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